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root/gclib/gclib/GAlnExtend.h
Revision: 186
Committed: Thu Feb 16 22:15:58 2012 UTC (7 years, 4 months ago) by gpertea
File size: 24517 byte(s)
Log Message:
adjust safelen threshold from 12 to 16

Line File contents
1 #ifndef _GALIGNEXTEND_H
2
3 //greedy gapped alignment extension
4 //(mostly lifted from NCBI's megablast gapped extension code)
5
6 #include "GBase.h"
7 #include "GList.hh"
8 #include "gdna.h"
9
10 //#define GDEBUG 1
11
12 enum {
13 gxEDIT_OP_MASK = 0x3,
14 gxEDIT_OP_ERR = 0x0,
15 gxEDIT_OP_INS = 0x1,
16 gxEDIT_OP_DEL = 0x2,
17 gxEDIT_OP_REP = 0x3
18 };
19
20 #define GX_EDITOP_VAL(op) ((op) >> 2)
21 #define GX_EDITOP_GET(op) ((op) & gxEDIT_OP_MASK)
22 #define GX_EDITOP_CONS(op, val) (((val) << 2) | ((op) & gxEDIT_OP_MASK))
23
24 #ifdef GDEBUG
25 enum {c_black=0,
26 c_red, c_green,c_brown,c_blue,c_magenta,c_cyan,c_white
27 };
28
29 void color_fg(int c, FILE* f=stderr);
30 void color_bg(int c, FILE* f=stderr);
31 void color_resetfg(FILE* f=stderr);
32 void color_resetbg(FILE* f=stderr);
33 void color_reset(FILE* f=stderr);
34 void color_normal(FILE* f=stderr);
35 #endif
36
37 struct GXEditScript{
38 uint32 *ops; // array of edit operations
39 uint32 opsize, opnum; // size of allocation, number in use
40 uint32 oplast; // most recent operation added
41 //methods
42
43 GXEditScript() {
44 init();
45 }
46 ~GXEditScript() {
47 GFREE(ops);
48 }
49 void init() {
50 ops = NULL;
51 opsize = 0;
52 opnum = 0;
53 oplast = 0;
54 getReady(8);
55 }
56
57 int getReady(uint32 n) {
58 uint32 m = n + n/2;
59 if (opsize <= n) {
60 GREALLOC(ops, m*sizeof(uint32));
61 opsize = m;
62 }
63 return 1;
64 }
65
66 int getReady2(uint32 n) {
67 if (opsize - opnum <= n)
68 return getReady(n + opnum);
69 return 1;
70 }
71
72 int Put(uint32 op, uint32 n) {
73 if (!getReady2(2))
74 return 0;
75 oplast = op;
76 ops[opnum] = GX_EDITOP_CONS(op, n);
77 opnum += 1;
78 ops[opnum] = 0; // sentinel
79 return 1;
80 }
81 uint32* First() {
82 return opnum > 0 ? & ops[0] : NULL;
83 }
84
85 uint32* Next(uint32 *op) {
86 // assumes flat address space !
87 if (&ops[0] <= op && op < &ops[opnum-1])
88 return op+1;
89 else
90 return 0;
91 }
92
93 int More(uint32 op, uint32 k) {
94 if (op == gxEDIT_OP_ERR) {
95 GError("GXEditScript::opMore: bad opcode %d:%d", op, k);
96 return -1;
97 }
98
99 if (GX_EDITOP_GET(oplast) == op) {
100 uint32 l=ops[opnum-1];
101 ops[opnum-1]=GX_EDITOP_CONS((GX_EDITOP_GET(l)),
102 (GX_EDITOP_VAL(l) + k));
103 }
104 else {
105 Put(op, k);
106 }
107
108 return 0;
109 }
110
111 GXEditScript* Append(GXEditScript *et) {
112 uint32 *op;
113 for (op = et->First(); op; op = et->Next(op))
114 More(GX_EDITOP_GET(*op), GX_EDITOP_VAL(*op));
115 return this;
116 }
117
118 int opDel(uint32 k) {
119 return More(gxEDIT_OP_DEL, k);
120 }
121 int opIns(uint32 k) {
122 return More(gxEDIT_OP_INS, k);
123 }
124 int opRep(uint32 k) {
125 return More(gxEDIT_OP_REP, k);
126 }
127
128 GXEditScript *reverse() {
129 const uint32 mid = opnum/2;
130 const uint32 end = opnum-1;
131 for (uint32 i = 0; i < mid; ++i) {
132 const uint32 t = ops[i];
133 ops[i] = ops[end-i];
134 ops[end-i] = t;
135 }
136 return this;
137 }
138 };
139
140
141 /** Bookkeeping structure for greedy alignment. When aligning
142 two sequences, the members of this structure store the
143 largest offset into the second sequence that leads to a
144 high-scoring alignment for a given start point */
145 struct SGreedyOffset {
146 int insert_off; // Best offset for a path ending in an insertion
147 int match_off; // Best offset for a path ending in a match
148 int delete_off; // Best offset for a path ending in a deletion
149 };
150
151 // ----- pool allocator -----
152 // works as a linked list of allocated memory blocks
153 struct GXMemPool {
154 SGreedyOffset* memblock;
155 int used, size;
156 GXMemPool *next;
157 static int kMinSpace;
158 //methods
159 GXMemPool(int num_offsp=0) { //by default allocate a large block here (10M)
160 num_offsp=GMAX(kMinSpace, num_offsp);
161 GMALLOC(memblock, num_offsp*sizeof(SGreedyOffset));
162 if (memblock == NULL) {
163 GError("Failed to allocated GXMemPool(%d) for greedy extension!\n",num_offsp);
164 return;
165 }
166 used = 0;
167 size = num_offsp;
168 next = NULL;
169 }
170
171 void refresh() {
172 GXMemPool* sp=this;
173 while (sp) {
174 sp->used = 0;
175 sp = sp->next;
176 }
177 }
178 ~GXMemPool() {
179 GXMemPool* next_sp;
180 GXMemPool* sp=this->next;
181 while (sp) {
182 next_sp = sp->next;
183 GFREE(sp->memblock);
184 delete sp;
185 sp = next_sp;
186 }
187 GFREE(memblock);
188 }
189
190 SGreedyOffset* getSpace(int num_alloc) { // SGreedyOffset[num_alloc] array
191 //can use the first found memory block with enough room,
192 // or allocate a new large block
193 SGreedyOffset* v;
194 if (num_alloc < 0) return NULL;
195 GXMemPool* S=this;
196 while (used+num_alloc > S->size) {
197 //no room in current block, get a new mem block
198 if (next == NULL) {
199 next=new GXMemPool(num_alloc); //allocates a large contiguous memory block
200 }
201 S = S->next;
202 }
203 v = S->memblock+S->used;
204 S->used += num_alloc;
205 //align to first 8-byte boundary
206 int m8 = S->used & 7; //modulo 8
207 if (m8)
208 S->used += 8 - m8;
209 return v;
210 }
211
212 void* getByteSpace(int byte_size) { //amount to use or allocate memory, in bytes
213 return (void*)getSpace(byte_size/sizeof(SGreedyOffset));
214 }
215
216 };
217
218 #define GREEDY_MAX_COST_FRACTION 8
219 /* (was 2) sequence_length / (this number) is a measure of how hard the
220 alignment code will work to find the optimal alignment; in fact
221 this gives a worst case bound on the number of loop iterations */
222
223 #define GREEDY_MAX_COST 1000
224 // The largest diff distance (max indels+mismatches) to be examined for an optimal alignment
225 // (should be increased for large sequences)
226
227 #define GX_GALLOC_ERROR "Error: failed to allocate memory for greedy alignment!\n"
228
229 // all auxiliary memory needed for the greedy extension algorithm
230 class CGreedyAlignData {
231 int d_diff;
232 int max_d;
233 public:
234 int** last_seq2_off; // 2-D array of distances
235 int* max_score; // array of maximum scores
236 GXMemPool* space; // local memory pool for SGreedyOffset structs
237 //
238 int match_reward;
239 int mismatch_penalty;
240 int x_drop;
241 // Allocate memory for the greedy gapped alignment algorithm
242 CGreedyAlignData(int reward, int penalty, int xdrop) {
243 //int max_d, diff_d;
244 if (penalty<0) penalty=-penalty;
245 if (reward % 2) {
246 //scale params
247 match_reward = reward << 1;
248 mismatch_penalty = (penalty << 1);
249 x_drop = xdrop<<1;
250 }
251 else {
252 match_reward=reward;
253 mismatch_penalty = penalty;
254 x_drop=xdrop;
255 }
256 //if (gap_open == 0 && gap_extend == 0)
257 // gap_extend = (reward >> 1) + penalty;
258 const int max_dbseq_length=255; //adjust this accordingly
259 max_d = GMIN(GREEDY_MAX_COST,
260 (max_dbseq_length/GREEDY_MAX_COST_FRACTION + 1));
261
262 last_seq2_off=NULL; // 2-D array of distances
263 max_score=NULL; // array of maximum scores
264 space=NULL; // local memory pool for SGreedyOffset structs
265 //if (score_params.gap_open==0 && score_params.gap_extend==0) {
266 //non-affine, simpler Greedy algorithm
267 d_diff = (x_drop+match_reward/2)/(mismatch_penalty+match_reward)+1;
268 GMALLOC(last_seq2_off, ((max_d + 2) * sizeof(int*)));
269 if (!last_seq2_off)
270 GError(GX_GALLOC_ERROR);
271 GCALLOC(last_seq2_off[0], ((max_d + max_d + 6) * sizeof(int) * 2));
272 //allocates contiguous memory for 2 rows here
273 if (!last_seq2_off[0])
274 GError(GX_GALLOC_ERROR);
275 last_seq2_off[1] = last_seq2_off[0] + max_d + max_d + 6; //memory allocated already for this row
276
277 GCALLOC(max_score, (sizeof(int) * (max_d + 1 + d_diff)));
278 space = new GXMemPool();
279 if (!max_score || !space)
280 GError(GX_GALLOC_ERROR);
281 } //consructor
282
283 void reset() {
284 space->refresh();
285 if (last_seq2_off) {
286 GFREE((last_seq2_off[0]));
287 }
288 GFREE(max_score);
289 GCALLOC(last_seq2_off[0], ((max_d + max_d + 6) * sizeof(int) * 2));
290 if (!last_seq2_off[0]) GError(GX_GALLOC_ERROR);
291 //allocates contiguous memory for 2 rows here
292 last_seq2_off[1] = last_seq2_off[0] + max_d + max_d + 6;
293 GCALLOC(max_score, (sizeof(int) * (max_d + 1 + d_diff)));
294 if (!max_score) GError(GX_GALLOC_ERROR);
295 }
296 ~CGreedyAlignData() {
297 if (last_seq2_off) {
298 GFREE(last_seq2_off[0]);
299 GFREE(last_seq2_off);
300 }
301 GFREE(max_score);
302 delete space;
303 }
304
305 };
306
307
308 #define GAPALIGN_SUB ((unsigned char)0) /*op types within the edit script*/
309 #define GAPALIGN_INS ((unsigned char)1)
310 #define GAPALIGN_DEL ((unsigned char)2)
311 #define GAPALIGN_DECLINE ((unsigned char)3)
312
313 struct GapXEditScript {
314 unsigned char op_type; // GAPALIGN_SUB, GAPALIGN_INS, or GAPALIGN_DEL
315 int num; // Number of operations
316 GapXEditScript* next;
317 GapXEditScript() {
318 op_type=0;
319 num=0;
320 next=NULL;
321 }
322 void print();
323 };
324
325 class CSeqGap { //
326 public:
327 int offset;
328 int len;
329 CSeqGap(int gofs=0,int glen=1) {
330 offset=gofs;
331 len=glen;
332 }
333 };
334
335 class CAlnGapInfo {
336 int a_ofs; //alignment start on seq a (0 based)
337 int b_ofs; //alignment start on seq b (0 based)
338 int a_len; //length of alignment on seq a
339 int b_len; //length of alignment on seq b
340 public:
341 GVec<CSeqGap> a_gaps;
342 GVec<CSeqGap> b_gaps;
343 CAlnGapInfo(GXEditScript* ed_script, int astart=0, int bstart=0):a_gaps(),b_gaps() {
344 a_ofs=astart;
345 b_ofs=bstart;
346 a_len=0;
347 b_len=0;
348 if (ed_script==NULL) return;
349 for (uint32 i=0; i<ed_script->opnum; i++) {
350 int num=((ed_script->ops[i]) >> 2);
351 char op_type = 3 - ( ed_script->ops[i] & gxEDIT_OP_MASK );
352 if (op_type == 3 || op_type < 0 )
353 GError("Error: encountered op_type %d in ed_script?!\n", (int)op_type);
354 CSeqGap gap;
355 switch (op_type) {
356 case GAPALIGN_SUB: a_len+=num;
357 b_len+=num;
358 break;
359 case GAPALIGN_INS: a_len+=num;
360 gap.offset=b_ofs+b_len;
361 gap.len=num;
362 b_gaps.Add(gap);
363 break;
364 case GAPALIGN_DEL: b_len+=num;
365 gap.offset=a_ofs+a_len;
366 gap.len=num;
367 a_gaps.Add(gap);
368 break;
369 }
370 }
371 }
372
373 #ifdef GDEBUG
374 void printAlignment(FILE* f, const char* sa, int sa_len,
375 const char* sb, int sb_len) {
376 //print seq A
377 char al[1024]; //display buffer for seq A
378 int ap=0; //index in al[] for current character printed
379 int g=0;
380 int aend=a_ofs+a_len;
381 if (a_ofs<b_ofs) {
382 for (int i=0;i<b_ofs-a_ofs;i++) {
383 fprintf(f, " ");
384 al[++ap]=' ';
385 }
386 }
387 for (int i=0;i<aend;i++) {
388 if (g<a_gaps.Count() && a_gaps[g].offset==i) {
389 for (int j=0;j<a_gaps[g].len;j++) {
390 fprintf(f, "-");
391 al[++ap]='-';
392 }
393 g++;
394 }
395 if (i==a_ofs) color_bg(c_blue,f);
396 fprintf(f, "%c", sa[i]);
397 al[++ap]=sa[i];
398 }
399 color_reset(f);
400 if (aend<sa_len)
401 fprintf(f, &sa[aend]);
402 fprintf(f, "\n");
403 //print seq B
404 ap=0;
405 g=0;
406 int bend=b_ofs+b_len;
407 if (a_ofs>b_ofs) {
408 for (int i=0;i<a_ofs-b_ofs;i++) {
409 fprintf(f, " ");
410 ap++;
411 }
412 }
413 for (int i=0;i<b_ofs;i++) {
414 fprintf(f, "%c", sb[i]);
415 ap++;
416 }
417 for (int i=b_ofs;i<bend;i++) {
418 if (g<b_gaps.Count() && b_gaps[g].offset==i) {
419 for (int j=0;j<b_gaps[g].len;j++) {
420 fprintf(f, "-");
421 ap++;
422 }
423 g++;
424 }
425 if (i==b_ofs) color_bg(c_blue,f);
426 ap++;
427 bool mismatch=(sb[i]!=al[ap] && al[ap]!='-');
428 if (mismatch) color_bg(c_red,f);
429 fprintf(f, "%c", sb[i]);
430 if (mismatch) color_bg(c_blue,f);
431 }
432 color_reset(f);
433 if (bend<sb_len)
434 fprintf(f, &sb[bend]);
435 fprintf(f, "\n");
436 }
437 #endif
438 };
439
440 struct GXAlnInfo {
441 const char *qseq;
442 int ql,qr;
443 const char *sseq;
444 int sl,sr;
445 int score;
446 double pid;
447 bool strong;
448 GXEditScript* editscript;
449 CAlnGapInfo* gapinfo;
450 GXAlnInfo(const char* q, int q_l, int q_r, const char* s, int s_l, int s_r,
451 int sc=0, double percid=0) {
452 qseq=q;
453 sseq=s;
454 ql=q_l;
455 qr=q_r;
456 sl=s_l;
457 sr=s_r;
458 score=sc;
459 pid=percid;
460 strong=false;
461 editscript=NULL;
462 gapinfo=NULL;
463 }
464 ~GXAlnInfo() {
465 delete editscript;
466 delete gapinfo;
467 }
468 bool operator<(GXAlnInfo& d) {
469 return ((score==d.score)? pid>d.pid : score>d.score);
470 }
471 bool operator==(GXAlnInfo& d) {
472 return (score==d.score && pid==d.pid);
473 }
474
475 };
476
477
478
479 struct GXSeed {
480 int b_ofs; //0-based coordinate on seq b (x coordinate)
481 int a_ofs; //0-based coordinate on seq a (y coordinate)
482 int len; //length of exact match after extension
483 bool operator<(GXSeed& d){
484 return ((b_ofs==d.b_ofs) ? a_ofs<d.a_ofs : b_ofs<d.b_ofs);
485 }
486 bool operator==(GXSeed& d){
487 return (b_ofs==d.b_ofs && a_ofs==d.a_ofs); //should never be the case, seeds are uniquely constructed
488 }
489 GXSeed(int aofs=0, int bofs=0, int l=4) {
490 a_ofs=aofs;
491 b_ofs=bofs;
492 len=l;
493 }
494 };
495
496 int cmpSeedDiag(const pointer p1, const pointer p2);
497 //seeds are "equal" if they're on the same diagonal (for selection purposes only)
498
499 int cmpSeedScore(const pointer p1, const pointer p2); //also takes position into account
500 //among seeds with same length, prefer those closer to the left end of the read (seq_b)
501
502 struct GXBand {
503 //bundle of seed matches on 3 adjacent diagonals
504 int diag; //first anti-diagonal (b_ofs-a_ofs) in this group of 3
505 //seeds for this, and diag+1 and diag+2 are stored here
506 int min_a, max_a; //maximal coordinates of the bundle
507 int min_b, max_b;
508 int w_min_b; //weighted average of left start coordinate
509 int avg_len;
510 GList<GXSeed> seeds; //sorted by x coordinate (b_ofs)
511 int score; //sum of seed scores (- overlapping_bases/2 - gaps)
512 bool tested;
513 GXBand(int start_diag=-1, GXSeed* seed=NULL):seeds(true, false, false) {
514 diag=start_diag;
515 min_a=MAX_INT;
516 min_b=MAX_INT;
517 max_a=0;
518 max_b=0;
519 score=0;
520 avg_len=0;
521 w_min_b=0;
522 tested=false;
523 if (seed!=NULL) addSeed(seed);
524 }
525 void addSeed(GXSeed* seed) {
526 seeds.Add(seed);
527 score+=seed->len;
528 avg_len+=seed->len;
529 w_min_b+=seed->b_ofs * seed->len;
530 //if (diag<0) diag=seed->diag; //should NOT be done like this
531 if (seed->a_ofs < min_a) min_a=seed->a_ofs;
532 if (seed->a_ofs+ seed->len > max_a) max_a=seed->a_ofs+seed->len;
533 if (seed->b_ofs < min_b) min_b=seed->b_ofs;
534 if (seed->b_ofs+seed->len > max_b) max_b=seed->b_ofs+seed->len;
535 }
536
537 void finalize() {
538 //!! to be called only AFTER all seeds have been added
539 // seeds are sorted by b_ofs
540 //penalize seed gaps and overlaps on b sequence
541 if (avg_len==0) return;
542 w_min_b/=avg_len;
543 avg_len>>=1;
544 for (int i=1;i<seeds.Count();i++) {
545 GXSeed& sprev=*seeds[i-1];
546 GXSeed& scur=*seeds[i];
547 if (scur==sprev) GError("Error: duplicate seeds found (%d-%d:%d-%d)!\n",
548 scur.a_ofs+1, scur.a_ofs+scur.len, scur.b_ofs+1, scur.b_ofs+scur.len);
549 int b_gap=scur.b_ofs-sprev.b_ofs-sprev.len;
550 int a_gap=scur.a_ofs-sprev.a_ofs-sprev.len;
551 int max_gap=b_gap;
552 int min_gap=a_gap;
553 if (min_gap>max_gap) Gswap(max_gap, min_gap);
554 int _penalty=0;
555 if (min_gap<0) { //overlap
556 if (max_gap>0) { _penalty=GMAX((-min_gap), max_gap); }
557 else _penalty=-min_gap;
558 }
559 else { //gap
560 _penalty=max_gap;
561 }
562 score-=(_penalty>>1);
563 //score-=_penalty;
564 }//for each seed
565 }
566
567 //bands will be sorted by decreasing score eventually, after all seeds are added
568 //more seeds better than one longer seed?
569 bool operator<(GXBand& d){
570 //return ((score==d.score) ? seeds.Count()>d.seeds.Count() : score>d.score);
571 return ((score==d.score) ? w_min_b<d.w_min_b : score>d.score);
572 }
573 bool operator==(GXBand& d){
574 //return (score==d.score && seeds.Count()==d.seeds.Count());
575 return (score==d.score && w_min_b==d.w_min_b);
576 }
577
578 };
579
580 class GXBandSet:public GList<GXBand> {
581 public:
582 GXSeed* qmatch; //long match (mismatches allowed) if a very good match was extended well
583 GXSeed* tmatch_r; //terminal match to be used if there is no better alignment
584 GXSeed* tmatch_l; //terminal match to be used if there is no better alignment
585 int idxoffset; //global anti-diagonal->index offset (a_len-1)
586 //used to convert a diagonal to an index
587 //diagonal is always b_ofs-a_ofs, so the minimum value is -a_len+1
588 //hence offset is a_len-1
589 GXBand* band(int diag) { //retrieve the band for given anti-diagonal (b_ofs-a_ofs)
590 return Get(diag+idxoffset);
591 }
592 GXBand* band(int a_ofs, int b_ofs) { //retrieve the band for given anti-diagonal (b_ofs-a_ofs)
593 return Get(b_ofs-a_ofs+idxoffset);
594 }
595 GXBandSet(int a_len, int b_len):GList<GXBand>(a_len+b_len-1, false, true, false) {
596 idxoffset=a_len-1;
597 qmatch=NULL;
598 tmatch_l=NULL; //terminal match to be used if everything else fails
599 tmatch_r=NULL;
600 //diag will range from -a_len+1 to b_len-1, so after adjustment
601 //by idxoffset we get a max of a_len+b_len-2
602 int bcount=a_len+b_len-1;
603 for (int i=0;i<bcount;i++)
604 this->Add(new GXBand(i-idxoffset));
605 //unsorted, this should set fList[i]
606 }
607 ~GXBandSet() {
608 delete qmatch;
609 }
610 void addSeed(GXSeed* seed) {
611 //MUST be unsorted !!!
612 int idx=(seed->b_ofs-seed->a_ofs)+idxoffset;
613 fList[idx]->addSeed(seed);
614 if (idx>0) fList[idx-1]->addSeed(seed);
615 if (idx<fCount-1) fList[idx+1]->addSeed(seed);
616 }
617 };
618
619 struct GXSeqData {
620 const char* aseq;
621 int alen;
622 const char* bseq;
623 int blen;
624 GVec<uint16>** amers;
625 int amlen; //minimum alignment length that's sufficient to
626 //trigger the quick extension heuristics
627 GXSeqData(const char* sa=NULL, int la=0, const char* sb=NULL, int lb=0,
628 GVec<uint16>* mers[]=NULL):aseq(sa), alen(la),
629 bseq(sb), blen(lb), amers(mers), amlen(0) {
630 calc_amlen();
631 calc_bmlen();
632 }
633 void calc_amlen() {
634 if (alen) {
635 int ah=iround(double(alen)*0.8);
636 if (ah<16) ah=16;
637 if (amlen>ah) amlen=ah;
638 }
639 }
640 void calc_bmlen() {
641 if (blen) {
642 int bh = iround(double(alen)*0.6);
643 if (bh<16) bh=16;
644 if (amlen>bh) amlen=bh;
645 }
646 }
647 void update(const char* sa, int la, GVec<uint16>** mers,
648 const char* sb, int lb, int mlen=0) {
649 aseq=sa;
650 alen=la;
651 amers=mers;
652 if (mlen) {
653 amlen=mlen;
654 }
655 else calc_amlen();
656 if (sb==bseq && blen==lb) return;
657 bseq=sb;
658 blen=lb;
659 calc_bmlen();
660 }
661 /*
662 void update_b(const char* sb, int lb) {
663 if (sb==bseq && blen==lb) return;
664 bseq=sb;
665 blen=lb;
666 calc_bmlen();
667 }*/
668 };
669
670 uint16 get6mer(char* p);
671 void table6mers(const char* s, int slen, GVec<uint16>* amers[]);
672
673 //GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, GXSeqData& sd); //for overlap at 3' end of seqb
674
675 GXBandSet* collectSeeds(GList<GXSeed>& seeds, GXSeqData& sd); //for overlap at 5' end of seqb
676
677 void printEditScript(GXEditScript* ed_script);
678
679
680 int GXGreedyExtend(const char* seq1, int len1,
681 const char* seq2, int len2,
682 bool reverse, int xdrop_threshold,
683 int match_cost, int mismatch_cost,
684 int& seq1_align_len, int& seq2_align_len,
685 CGreedyAlignData& aux_data,
686 GXEditScript *edit_block);
687
688
689 enum GAlnTrimType {
690 //Describes trimming intent
691 galn_None=0, //no trimming, just alignment
692 galn_TrimLeft,
693 galn_TrimRight,
694 galn_TrimEither //adaptor should be trimmed from either end
695 };
696
697 struct CAlnTrim {
698 GAlnTrimType type;
699 int l_boundary; //base index (either left or right) excluding terminal poly-A stretches
700 int r_boundary; //base index (either left or right) excluding terminal poly-A stretches
701 int alen; //query/adaptor seq length (for validate())
702 int safelen; //alignment length > amlen should be automatically validated
703 int seedlen;
704 void prepare(const char* s, int s_len) {
705 //type=trim_type;
706 //amlen=smlen;
707 l_boundary=0;
708 r_boundary=0;
709 //if (type==galn_TrimLeft) {
710 int s_lbound=0;
711 if (s[0]=='A' && s[1]=='A' && s[2]=='A') {
712 s_lbound=3;
713 while (s_lbound<s_len-1 && s[s_lbound]=='A') s_lbound++;
714 }
715 else if (s[1]=='A' && s[2]=='A' && s[3]=='A') {
716 s_lbound=4;
717 while (s_lbound<s_len-1 && s[s_lbound]=='A') s_lbound++;
718 }
719 l_boundary=s_lbound+3;
720 // return;
721 // }
722 //if (type==galn_TrimRight) {
723 int r=s_len-1;
724 if (s[r]=='A' && s[r-1]=='A' && s[r-2]=='A') {
725 r-=3;
726 while (r>0 && s[r]=='A') r--;
727 }
728 else if (s[r-1]=='A' && s[r-2]=='A' && s[r-3]=='A') {
729 r-=4;
730 while (r>0 && s[r]=='A') r--;
731 }
732 r_boundary=r-3;
733 // }
734 }
735
736 CAlnTrim(GAlnTrimType trim_type, const char* s, int s_len, int a_len, int smlen):
737 type(trim_type), l_boundary(0), r_boundary(0), alen(a_len), safelen(smlen) {
738 prepare(s, s_len);
739 }
740
741 bool validate_R(int sr, int admax, int badj, int adist) {
742 if (adist>admax) return false;
743 return (sr>=r_boundary+badj);
744 }
745
746 bool validate_L(int sl, int alnlen, int admax, int badj, int alnpid, int adist) {
747 if (adist>admax) return false;
748 //left match should be more stringent (5')
749 if (alnpid<93) {
750 if (alnlen<13) return false;
751 admax=0;
752 badj++;
753 }
754 return (sl<=l_boundary-badj);
755 }
756
757 bool validate(GXAlnInfo* alninfo) {
758 int alnlen=alninfo->sr - alninfo->sl + 1;
759 if (alninfo->pid>90.0 && alnlen>safelen) {
760 //special case: heavy match, could be in the middle
761 if (alninfo->pid>94)
762 alninfo->strong=true;
763 return true;
764 }
765 int sl=alninfo->sl;
766 int sr=alninfo->sr;
767 sl--;sr--; //boundary is 0-based
768 int badj=0; //default boundary is 3 bases distance to end
769 int admax=1;
770 if (alnlen<13) {
771 //stricter boundary check
772 if (alninfo->pid<90) return false;
773 badj=2;
774 if (alnlen<=7) { badj++; admax=0; }
775 }
776 if (type==galn_TrimLeft) {
777 return validate_L(sl, alnlen, admax, badj, alninfo->pid, alen-alninfo->qr);
778 }
779 else if (type==galn_TrimRight) {
780 return validate_R(sr, admax, badj, alninfo->ql-1);
781 }
782 else if (type==galn_TrimEither) {
783 return (validate_R(sr, admax, badj, alninfo->ql-1) ||
784 validate_L(sl, alnlen, admax, badj, alninfo->pid, alen-alninfo->qr));
785 }
786 return true;
787 /*
788 if (type==galn_TrimRight) {
789 return (sr>=boundary+badj);
790 }
791 else {
792 //left match should be more stringent (5')
793 if (alnpid<93) {
794 if (alnlen<13) return false;
795 admax=0;
796 badj++;
797 }
798 return (sl<=boundary-badj);
799 }
800 */
801 }
802 };
803
804
805 // reward MUST be >1, always
806 GXAlnInfo* GreedyAlignRegion(const char* q_seq, int q_alnstart, int q_max,
807 const char* s_seq, int s_alnstart, int s_max,
808 int reward, int penalty, int xdrop, CGreedyAlignData* gxmem=NULL,
809 CAlnTrim* trim=NULL, bool editscript=false);
810 GXAlnInfo* GreedyAlignRegion(const char* q_seq, int q_alnstart, int q_max,
811 const char* s_seq, int s_alnstart, int s_max, CGreedyAlignData* gxmem,
812 CAlnTrim* trim=NULL, bool editscript=false);
813
814 GXAlnInfo* GreedyAlign(const char* q_seq, int q_alnstart, const char* s_seq, int s_alnstart,
815 bool editscript=false, int reward=2, int penalty=3, int xdrop=8);
816
817 GXAlnInfo* match_adaptor(GXSeqData& sd, GAlnTrimType trim_type,
818 CGreedyAlignData* gxmem=NULL, int min_pid=90);
819 //GXAlnInfo* match_RightEnd(GXSeqData& sd, CGreedyAlignData* gxmem=NULL, int min_pid=90);
820 #endif